title: Study on the interaction of homoisoflavonoids with RNA.
abstract: Homoisoflavonoids (3-benzylidene-4-chromanones) are isomers of flavonoids and exhibit different biological activities because of hydroxyl groups attaching to different positions. This study is the first attempt to locate the binding sites of four synthetic homoisoflavonoids: (E)-3-(3,4-dihydroxybenzylidene)-7-methoxychroman-4-one (BMC), (E)-3-(3,4-dihydroxybenzylidene)-7-propoxychroman-4-one (BPC), (E)-3-(4-hydroxybenzylidene)-7-methoxychroman-4-one (HBMC) and (E) 3-(4-hydroxybenzylidene)-chroman-4-one (HBC) to RNA. The effect of the ligand complexation on RNA aggregation was investigated in aqueous solution at physiological conditions, using constant RNA concentration (6.25mM) and various ligand/polynucleotide (phosphate) ratios of 1/120, 1/80, 1/40, 1/20, 1/10 and 1/5. Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of ligand-RNA complexes in aqueous solution. Spectroscopic evidence showed external binding of homoisoflavonoids to RNA duplex with overall binding constants of KBMC-RNA = 1.06(± 0.09) × 10(4)M(-1), KBPC-RNA = 1.11(± 0.15) × 10(4)M (-1), KHBC-RNA = 3.82(± 0.09) × 10(3)M(-1) and KHBMC-RNA=5.82(± 0.04) × 10(3) M(-1). The affinity of homoisoflavonoid-RNA binding is in the order of BPC>BMC>HBMC>HBC. No biopolymer secondary structural changes were observed upon homoisoflavonoids interaction and RNA remains in the A-family structure in these complexes.
authors.affiliation: Department of Chemistry, Islamic Azad University, Central Tehran Branch (IAUCTB), Tehran, Iran; Young Researchers and Elite Club, Central Tehran Branch, Islamic Azad University, Tehran, Iran.
authors.forename: Roshanak
authors.initials: R
authors.lastname: Namdar
authors.forename: Neda
authors.initials: N
authors.lastname: Makouie
authors.forename: Shohreh
authors.initials: S
authors.lastname: Nafisi
mesh_terms: D001665:Binding Sites; D007529:Isoflavones / Q000737:chemistry*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012331:RNA, Fungal / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013056:Spectrophotometry, Ultraviolet; D017550:Spectroscopy, Fourier Transform Infrared; D013237:Stereoisomerism
chemical_list: D007529:Isoflavones; D012331:RNA, Fungal; D012313:RNA
keywords: 3-Benzylidenechroman-4-ones; FTIR; Homoisoflavonoids; RNA; UV–Visible spectroscopy